We studied changes in brain volume on magnetic resonance imaging in 10 patients with and without EC-IC bypass surgery who met the inclusion criteria for the Japanese EC-IC bypass trial, a multicenter, randomized, double-blind, prospective study of patients with hemodynamic brain ischemia due to cerebral artery occlusive disease. We also examined the association of cerebral hemodynamics on single photon emission computed tomography with the changes in brain volume. As a result, the affected/unaffected ratio of the % brain volume declined in patients without EC-IC bypass surgery (p < 0.02, n = 4), and the affected/unaffected % rCBF ratio increased in patients with the surgery (p < 0.03, n = 6). Acetazolamide reactivity increased in the affected hemisphere of patients with surgery (p < 0.01). And also two-year increase (decrease) in acetazolamide reactivity of the affected hemisphere showed a significant positive correlation with 2-year changes in the affected/unaffected % brain volume ratio (R2 = 0.737, p = 0.0007). Change in acetazolamide reactivity might be a good predictor for brain atrophy in cerebral artery occlusive disease.